After a cloud of swarming locusts descends upon Great Valley, devouring all plants and leaving it a barren wasteland, the inhabitants must seek another place where they can survive until the plants in Great Valley have grown back. However, the Leaf Gobblers have left a path of devastation behind them, leaving no food for the dinosaurs to find. After erring for days and days through this desolation, the herd quarrel and threaten to separate. The main characters do not want to be separated, so they set out to find a location with plentiful food. They leave a trail for the grownups to find them with, and eventually reach the "Big Water" (ocean). There, they see a verdant island connected to the mainland by a thin land bridge. On their way, a Tsunami occurs, which they narrowly escape, and which wipes out the bridge.
Isolated on the island, they try out Cera's idea to return by using a log as a boat (which made her seasick). However, a Megalodon ("swimming sharptooth") attacks, and in the confusion and fright which follows, they end up on the island again. That night, they remember their families, while the herd, who followed the trail, sleep on the shores of the beach on the mainland, worrying for them.
The next morning, the children and Tino and the others wake up to the shadow of a Sharptooth. They take off, but find themselves cornered by high cliffs. They huddle together when the sharptooth approaches, only to find that it is Chomper (from Tino's Adventures of The Land Before Time II: The Great Valley Adventure) and Bliss (from The Powerpuff Girls (2016). They then helps them to hide from his parents (he can talk now unlike before when he was a baby), who are also on the island, and provides them with food upon their request. However, an overcautious Cera openly displays distrust to Chomper because he was a Sharptooth, which grieves him, and he departs. Littlefoot follows him and apologizes, but is interrupted by Chomper's mother. She nuzzles him, then leaves, presuming Littlefoot is prey. Littlefoot is intrigued by her display of love to Chomper.
Meanwhile, another Sharptooth Giganotosaurus living on the island finds the children and our heroes, and gives them chase. Chomper tries to help, but the Giganotosaurus overcomes him. His parents then come and battle the Giganotosaurus near the edge of the island, during which he falls into the Big Water and takes Chomper with him. Littlefoot plunges in to save Chomper while the Giganotosaurus is swept away by the current. Another "swimming sharptooth" appears, but they discover it was an Elasmosaurus named Elsie who then saves the two from drowning. She returns them to the island, where Chomper's grateful family promises never to harm the children and Tino and the others. Still, the gang miss their families, so Elsie offers to take them across the sea, making Cera even more seasick than before. They say their final goodbyes to Chomper and Sophia, and board Elsie. When back on the mainland, they find out that the herd found a lush, green, little place on the shore to stay in till the Great Valley is green again.
- Blisstina "Bliss" Utonium, Twilight Sparkle, Applejack, Rarity, Rainbow Dash, Pinkie Pie, Fluttershy, Spike, The Cutie Mark Crusaders, Thomas the Tank Engine, and Percy guest stars in this film.
- Jason Marsden as Tino Tonitini
- Grey DeLisle as Lor McQuarrie
- Phil LaMarr as Carver Descartes
- Kate Soucie as Tish Katsufrakis
- Mona Marshall as Doraemon
- Johnny Yong Bosch as Noby Nobi
- Cassandra Morris as Sue
- Brian Beacock as Sneech
- Kaiji Tang as Takeshi "Big G" Goda
- Joseph May as Thomas the Tank Engine
- Christopher Ragland as Percy
- Tara Strong as Twilight Sparkle
- Ashleigh Ball as Rainbow Dash / Applejack
- Andrea Libman as Pinkie Pie / Fluttershy
- Tabitha St. Germain as Rarity
- Cathy Weseluck as Spike the Dragon
- Michelle Creber as Apple Bloom
- Claire Corlett as Sweetie Belle
- Madeleine Peters as Scootaloo
- Scott McAfee as Littlefoot
- Candace Hutson as Cera
- Heather Hogan as Ducky
- Jeff Bennett as Petrie / Mr. Clubtail
- Rob Paulsen as Spike
- Cannon Young as Chomper
- Kenneth Mars as Grandpa Longneck
- Miriam Flynn as Grandma Longneck
- Christina Pickles as Elsie
- John Ingle as Narrator / Cera's Father
- Tress MacNeille as Ducky's Mother / Petrie's Mother